Does FLIP fluid support more then one domain in one scene?
The FLIP Fluids addon does not support more than one domain in a .blend file at the moment. A workaround to have multiple simulation animations in a scene is to export the simulation to the Alembic format through File > Export > Alembic (.abc). Once exported, you can import the animated Alembic files back into your scene.

More information can be found in this documentation topic: https://github.com/rlguy/Blender-FLIP-Fluids/wiki/Alembic-Export-Support